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- PDB-8b2v: Millisecond cryo-trapping by the spitrobot crystal plunger, CTX-M... -

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Basic information

Entry
Database: PDB / ID: 8b2v
TitleMillisecond cryo-trapping by the spitrobot crystal plunger, CTX-M-14 E166A Ampicillin, 1 sec
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / CTX-M-14 / time-resolved crystallography
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AIX / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsMehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Doepke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. ...Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Doepke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / Tellkamp, F. / Schulz, E.C.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2023
Title: Millisecond cryo-trapping by the spitrobot crystal plunger simplifies time-resolved crystallography.
Authors: Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / ...Authors: Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / Tellkamp, F. / Schulz, E.C.
History
DepositionSep 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9522
Polymers27,6001
Non-polymers3511
Water3,387188
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.877, 41.877, 232.904
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Beta-lactamase


Mass: 27600.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ctx-m-14 / Production host: Escherichia coli (E. coli) / References: UniProt: D2D9A0, beta-lactamase
#2: Chemical ChemComp-AIX / (2R,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / AMPICILLIN (open form)


Mass: 351.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 4.5 / Details: 40% PEG8000, 200 mM LiSO4, 100 mM NaOAc, pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.728→77.635 Å / Num. obs: 14503 / % possible obs: 80.2 % / Redundancy: 12.5 % / Biso Wilson estimate: 13.99 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.9
Reflection shellResolution: 1.728→1.998 Å / Num. unique obs: 726 / CC1/2: 0.724

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6gth

6gth


Resolution: 1.73→38.82 Å / SU ML: 0.1725 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.0066
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2475 743 5.12 %
Rwork0.2005 13760 -
obs0.2029 14503 55.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.85 Å2
Refinement stepCycle: LAST / Resolution: 1.73→38.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 24 188 2149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00332079
X-RAY DIFFRACTIONf_angle_d0.67262845
X-RAY DIFFRACTIONf_chiral_restr0.0461331
X-RAY DIFFRACTIONf_plane_restr0.0065381
X-RAY DIFFRACTIONf_dihedral_angle_d11.0469303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.860.4164290.2841409X-RAY DIFFRACTION8.61
1.86-2.050.3596360.2623668X-RAY DIFFRACTION13.92
2.08-2.350.29611320.24663209X-RAY DIFFRACTION75.59
2.35-2.950.26512490.22194590X-RAY DIFFRACTION92.72
2.95-38.820.21882970.16944884X-RAY DIFFRACTION93.84
Refinement TLS params.Method: refined / Origin x: 5.90653460564 Å / Origin y: -1.47993691829 Å / Origin z: 19.7054976744 Å
111213212223313233
T0.148602669523 Å20.075736992513 Å2-0.00281039920513 Å2-0.0853063807089 Å2-0.0121278361823 Å2--0.082212137319 Å2
L0.198907279985 °20.181078782802 °2-0.264743390303 °2-0.890506021029 °2-1.03518237568 °2--3.18114464928 °2
S0.0274858986257 Å °0.00426586627298 Å °-0.0610417652588 Å °-0.162136790955 Å °-0.0277394492401 Å °-0.0170886914061 Å °0.448895452589 Å °0.276262645146 Å °-0.00797939934206 Å °
Refinement TLS groupSelection details: all

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